biopython/biopython — pull request #450 by widdowquinn (2014-12-19 18:35:31+00:00)
Title: Kgml bugfix

The hexdarken function expected a hex-encoded colour, rather than the usual ReportLab colours, but was only used for foreground colouring, so assignments of ReportLab colours slipped past the tests. I renamed the function to darken() [there should be no downstream side-effects] and changed all calls in this file, appropriately. I also modified darken() so that it tests for hex- or RGB colour encoding, and returns a darkened colour of the same type.

The show_reaction_entries option was necessary because it was not possible to entirely remove ortholog elements from KEGG maps without also removing reaction_entries elements. The previous code did not allow for reaction_entries elements to be hidden, only their labels.